Polar cod (Boreogadus saida) is one of the most studied Arctic marine fishes given its circumpolar distribution and centralised role in the Arctic marine food web. In contrast, relatively little is known about two other Arctic Gadidae: saffron cod (Eleginus gracilis) and Greenland cod (Gadus ogac). Climate change is expected to have an effect on sea ice-associated species, such as polar cod, but due to our lack of knowledge of other arctic gadid species it remains unclear how climate change will impact them and their interactions within the arctic marine ecosystem. Here, we explored the ecology of three Arctic Gadidae that co-occur in the Canadian Beaufort Sea. Stable isotope (SI) (niche overlap) and fatty acid (FA) (correspondence analysis and linear discriminant analysis) biomarkers were used to assess among- and within-species differences and trophic niche. Despite the close habitat proximity of saffron cod and polar cod while on the shelf, trophic niche characterisation revealed only a marginal overlap. Marginal niche overlaps also occurred for the two coastal species with similar diets, saffron cod and Greenland cod, likely reflecting regional-scale differences between two habitats. Within-species, polar cod collected from three habitats (shelf, upper- and lower-slope habitats) were not differentiated likely due to the movement of individuals between habitats. In contrast, Greenland cod had a narrow trophic niche and differentiation occurred between the two collection sites. The comparison of trophic niches defined by stable isotope and fatty acid proved a promising tool for new insights into the ecology of Arctic fishes.